Tools developed by Moriyama lab



Multi-Objective Clustering Algorithm for Sequence Similarity Networks for proteins

Keel, B. H., Deng, B. and Moriyama, E. N. (2018) MOCASSIN-prot: A multiple objective clustering approach for protein similarity networks. Bioinformatics 34: 1270-1277.



Arabidopsis G-signaling Interactome Database

Klopffleisch, K., Phan, N., Augustin, K., Bayne, R. S., Booker, K. S., Botella, J. R., Carpita, N. C., Carr, T., Chen, J.-G., Cooke, T. R., Frick-Cheng, A., Friedman, E. J., Fulk, B., Hahn, M. G., Jiang, K., Jorda, L., Kruppe, L., Liu, C., Lorek, J., McCann, M. C., Molina, A., Moriyama, E. N., Mukhtar, M. S., Mudgil, Y., Pattathil, S., Schwarz, J., Seta, S., Tan, M., Temp, U., Trusov, Y., Urano, D., Welter, B., Yang, J., Panstruga, R., Uhrig, J. F. and Jones, A. M. (2011) Arabidopsis G protein interactome reveals connections to cell wall carbohydrates and morphogenesis. Molecular Systems Biology 7: 532.



A hierarchical mining tool for 7TMRs

Lu, G., Wang, Z., Jones, A. M., and Moriyama, E. N. (2009) 7TMRmine: A Web server for hierarchical mining of 7TMR proteins. BMC Genomics 10: 275.



Visual Tools for Multiple Sequence Alignment Comparison and Molecular Sequence Simulation

Anderson, C. L., Strope, C. L., and Moriyama, E. N. (2011) Assessing multiple sequence alignments using visual tools, in Bioinformatics: Trends and Methodologies (ed. Mahdavi, M. A.). InTech (ISBN 978-953-307-282-1)

Anderson, C. L., Strope, C. L. and Moriyama, E. N. (2011) SuiteMSA: Visual tools for multiple sequence alignment comparison and molecular sequence simulation. BMC Bioinformatics 12: 184



Simulated Protein Benchmark Database: large scale protein alignments

Catherine Anderson (2017) Selecting the "closest to optimal" multiple sequence alignment using multi-layer perceptron. PhD dissertation, Department of Computer Science and Engineering, University of Nebraska—Lincoln.



Fungal Genome Collection with Comparative Genomics Information

Wilson, R. A., Fernandez, J., Quispe, C. F., Gradnigo, J., Seng, A., Moriyama, E. N., and Wright, J. D. (2012) Towards defining nutrient conditions encountered by the rice blast fungus during host infection. PLoS ONE 7: e47392


indel-Seq-Gen (iSG)

A protein family simulator that can incorporate domains, motifs, and indels

Strope, C. L., Scott, S. D. and Moriyama, E. N. (2007) indel-Seq-Gen: a new protein family simulator incorporating domains, motifs, and indels. Mol Biol Evol 24: 640-649.

Strope, C. L., Abel, K., Scott, S. D., and Moriyama, E. N. (2009) Biological sequence simulation for testing complex evolutionary hypotheses: indel-Seq-Gen version 2.0. Mol Biol Evol 26: 2581-2593.

iSGv2.1.0 Benchmark Datasets

Large and highly divergent sequence sets generated by iSGv2.1.0

(last updated: June 10, 2018)

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